igem.org iGEM, The Registry of Standard Biological Parts, And Synthetic Biology Randy Rettberg Cambridge, UK July 5, 2010

igem.org Synthetic Biology Question Can simple biological systems be built from standard, interchangeable parts and operated in living cells? Or, is biology so complex that each case is unique?

igem.org Education Driving Research

igem.org Device-Level System Diagram 2003

igem.org Parts- and Device-Level System Diagram

igem.org iGEM Philosophy iGEM Philosophy: Get and Give Teams are expected to use the parts, ideas, and experience of teams in previous years. Teams are expected to contribute their parts, ideas, and experiences.

igem.org iGEM 2004 (SBC 04)

igem.org iGEM 2005

igem.org iGEM 2005

igem.org iGEM 2006

igem.org iGEM 2007

igem.org iGEM 2008

igem.org iGEM 2009

igem.org

iGEM 2010 Teams - 2

igem.org iGEM AND High School Teams  Advisor:Wendell Lim  Advisor:Orion Weiner  Advisor:James Onuffer  Teacher at Lincoln High School: George Cachianes  Teacher at Lincoln High School: Julie Reis  Plus 10 “Buddies”

igem.org Is iGEM Safe?

igem.org Is iGEM Secure?

igem.org IAP Year Teams Jamboree Total iGEM Growth and Scale iGEM Scale and Growth Or Not !

igem.org iGEM 2010 and Beyond − Teams, Jamboree at MIT November 6- 8 − (?) Teams, –Regional Jamborees in October –World Championship at MIT (Nov. 5-7) –Regional iGEM Headquarters −iGEM Labs and Courses –Sign up at ung.igem.org −iGEM Society, Institution, Foundation −iGEM Alumni Association

igem.org New Synthetic Biologists

igem.org Registry Labs

igem.org Synthetic Biology Courses

igem.org iGEM Community Now 7,041user accounts 6,513unique s 1,782users have logged in since Feb have entered parts 12,327 parts entered 5,166DNA samples at the Registry 2,328reported to work 1,691parts sent by last year’s teams 795sequence confirmed parts

igem.org The Registry: Quality Not Quantity Parts in the Registry are believed to be of low quality. 1.The DNA Sample does not match the part sequence or cannot be transformed. 2.The Part is not well documented in the Registry. 3.The Part has not been measured. 4.Interchangeable parts are not possible. 5.Lots of parts are junk.

igem.org Part Quality Parts in the Registry are believed to be of low quality. 1.The DNA Sample does not match the part sequence or cannot be transformed. –DNA Quality Control Program 2.The Part is not well documented in the Registry. –Curation, Ratings, Judges, Filtering 3.The Part has not been measured. –BioFab, Jason’s measurement program, Devices 4.Interchangeable parts are not possible. –BioLint 5.Lots of parts are junk –Delete, clean up, hide

igem.org BBa_K

igem.org BBa_K – Main Page

igem.org BBa_K – Get This Part

igem.org BBa_K Show 2 other locations

igem.org Extra PstI Site -

igem.org DNA Samples: Quality Control Program

igem.org Sample QC: Digest Gel

igem.org Sample QC: Antibiotic Test Plate

igem.org Sample QC: Sequence Analysis

igem.org Sample QC: Sample Provenance

igem.org The Registry – Pace of Change

igem.org May 2003

igem.org

partsregistry.org

igem.org Example Part

igem.org Parameters, Categories,...

igem.org Catalog Style 2009

igem.org Plasmids/Assembly

igem.org 2010 DNA Distribution 2010 Kit Plates Plasmid Backbones -pSB1C3 -pSB1T3 -pSB1A3 -Cut with EcoRI, PstI, and DpnI

igem.org 3A Assembly

igem.org Sample QC: Shipping Changes 1.Compatible with RFC10 (no EcoRI, XbaI,SpeI, PstI) 2.In pSB1C3 if possible, contact if not 3.Enter sequencing information 4.Use shipping form

igem.org Part Documentation – Not Good

igem.org Part Documentation – Vanillin p. 1

igem.org Part Documentation – Vanillin p. 2

igem.org Part Documentation – E0040 p. 1

igem.org Part Documentation – E0040 p. 2

igem.org Part Documentation – Why a Wiki

igem.org Part Documentation – Why a Wiki

igem.org Part Documentation – Why a Wiki

igem.org Part Documentation – Why a Wiki

igem.org Devices: A ‘Black Box’

igem.org Devices: Interfaces Primary Interfaces The intended functions of this device. Secondary Interfaces Materials required for the proper operation of this part or expected to be generated by this part. E.g. energy, waste Tertiary Interfaces Possible but unexpected interactions with the environment.

igem.org Devices: Main Page This device takes inputs and makes outputs according the proof of Fremat’s Last Theorem described in our team’s wiki. We ran out of time to complete the proof, but it is obvious to any capable undergraduate. Other applications of this device include universal cryptography, X-ray vision processing, and world peace. PinNameI/OTypeSubtype AGateInputPoPSURL:alllsdf.asdf. BNumberInputPoPSURL:allsdf.asfd CReadyInputIPTGURL:rsbp DResetInputHeatURL:rsbp.5900 EResultOutpurPoPSURL:alilsdf.asdf

igem.org Devices: Design This device consists of 3 different parts to compute magic numberskj kjlaalklkjf jaksalskdfj df f f as df f a sd f asd fad f asd f a sdf a df a sd f asd fad sf asdf asdf as df asdf as dfa dsf a sdf as dfas dfaksdjfklkrtf wt 5givi g hio ytf jopuiguyf iuhjii y uuhjoo jo hygyhijk oh ugy t rt y ii I I yt tg h jk I iuy f g hj k I y e 3 4 u jm k hf gh j

igem.org Devices: Other Interfaces −Examples include proteins used internal to the function of the part. −Sensitivities to DNA binding proteins −Required use of energy molecules

igem.org Devices: DNA Implementation DNA Segments A B C D

igem.org Devices: Representations SBML Model lksdjflL< klsdjflak Clotho Lkjfaiovunenzvncvnnn.vzvrvb cwkernfc fyhnkufhabcbxteqwxmc,vgbl,ih0upyt;lfdsnzgoi Empty

igem.org Devices: Measurement −Measurement values −Units (URI) −Measurement Protocol (URI) −Group (URI) −Measurement Batch ID (URI) −Comments

igem.org Devices: References −References

igem.org More Registries – A Web of Registries MIT iGEM in Asia iGEM in Europe SB Corp ASM SynBERC

igem.org Registry Version 4 Objects Tools MediaWiki Engine Hard Information Wiki Users mySQL

igem.org A 21 st Century Registry Design Syn-Bio-Co 1Syn-Bio-Co 2Public DataSchool 1Lab 1 Tool Viewer How can the interfaces be developed?

igem.org

External Tools ERC Meeting SynBERC Introduction

igem.org Key Issues −Getting Synthetic Biologists to add parts −Quality of the collection −Intellectual Property −Thousands of users – live −Timing −Integration with bioinformatics tools −Secrecy and limited access ?

igem.org Some Issues −How will the interfaces be developed? −Who gets to edit what? −Are there groups, user accounts, a user community? −Where does the software run? in the user’s PC, in the lab server, at a central site, in the “cloud” (at Google or Amazon) −How will pre-publication be handled? −Why will anyone share anything? −Will the core be a community or centralized development? −How will free-form content be supported?

igem.org Status of Synthetic Biology −Science, Engineering, and Industry – Cultures and Values −Arguments by analogy fail four times, why bother? −Failure to execute vs Failure to imagine −Representation in a young field −Community −1850 vs 2010: –Resistors, Capacitors, Inductors, Current Sources, Voltage Sources, Diodes, Transistors, Meters, Shielding, Ground Planes −Support −Centers for Systems and Synthetic Biology

igem.org Engineering Products – Apple Quadra 840AV “Ahead of its time, the 840AV and its relative, the Centris/Quadra 660AV, were the first Macintoshes to include 16-bit 48KHz stereo audio recording capability, as well as S-Video and Composite video input and output. They were also the first personal computers that supported speech recognition (PlainTalk) out- of-the-box.”

igem.org Voltmeter - Electronic

igem.org Voltmeter - Microbiology

igem.org Biologists Use - Jello ?

igem.org Good News - Soldering ~ Assembly BioBrick Standard Assembly - TK

igem.org Good News – Modularity Exists 434 cI RBS T LacI CI O Lac CI

igem.org Biological Insulation ?

igem.org Apple QuickTake – too early Apple QuickTake 100 introduced February 16, 1994, the Apple QuickTake 100 was one of the first consumer digital cameras. It came with a heafty price tag of $749 for a single focal length, fixed focus camera with maximum 640 x 480 resolution. Adjusted for inflation the price was nearly $1,100 in 2006 dollars. Shutter sppeds were 1/30 to 1/175 second. The QuickTake 100 could only be used directly with an Apple Mac. The later Quicktake 150, introduced May 1995, could also be used with a Windows PC. Both had only 1mb internal storage and no external storage. They could hold about 16 images before you had to download the images to the computer. Connection to the computer was with a round Apple serial cord. The QuickTake 100 and 150 were made by Kodak.

igem.org iPad way too early Apple PenLite (ATG 1992)

igem.org iGEM 2009

igem.org IAP Year Teams Jamboree Total iGEM Growth and Scale iGEM Scale and Growth Or Not !

igem.org Heidelberg 2008